The development and optimisation of food preservation processes seem to be necessary in order to address consumer expectations related to secure, fresh-like foods. To this end, the sensory, nutritional and functional properties must be maximally retained. In order to contribute to the acquisition of knowledge about the adequacy of microwave processing as a means of preserving fruit-based products, the present study compares the impact of microwave heating with conventional thermal processing. The consumer acceptance of fresh and pasteurised kiwifruit puree was studied as was the content of water, soluble solids and bioactive compounds and the pH, consistency, viscosity, colour coordinates and antioxidant capacity, as well as the effect of the thermal treatment on enzyme and microbial inactivation. As bioactive compounds, the content of vitamins C, A and E and the total flavonoid, phenol and tannin content have been considered. As the obtained results show, not only was microwaved puree preferred by consumers, but it also exhibited a superior maintenance of the nutritive and functional properties of the fruit, smaller colour changes and a content of inactivated enzymes and microorganisms equal to or greater than the conventionally heated sample.